Workflow

Click the nodes to obtain details about each step.

QC reads

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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# This file should contain everything to configure the workflow on a global scale.
# In case of sample based data, it should be complemented by a samples.tsv file that contains
# one row per sample.

sampletable: "config.tsv" ## 
path: "/home/lvelo/working_directory/microbiology/nat_comm_code/" ## folder that will contain the results
threads: 20
quality: 20
maxEE:
  - 2
  - 2
learn_nbases: 100e6
chimera_method: "pooled"
max_length_variation: 30     # how many nucleotide can a sequence be longer or shorter than the mode sequence length
HUMAN: "/PUBLIC_DATA/kraken2_databases/HUMAN"
silva: "/home/lvelo/working_directory/tax/silva_nr_v138_train_set.fa.gz"
silva_species: "/home/lvelo/working_directory/tax/silva_species_assignment_v138.fa.gz"
GTDB: "/home/lvelo/working_directory/tax/IDTaxa/GTDB_r95-mod_August2020.rdata"

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